The megazineSetup (which I have yet to write a tutorial about...) only works for swfs loaded via the img elements, so that's not an option here, I'm afraid.
The idea of adding a public function to the Main class should in fact work, you'll just have to make sure to address it properly. When loading the swf via a loader you'll have to use something like this:
function swfLoaded(e:Event):void {
var main:DisplayObject = myloader.getChildAt(0); // to get the actual instance of the Main class
main.yourPublicFunction();
}
If you can live without the features provided through the main class, though (SWFAddress, console, ...) you could just create a new instance, though, instead of loading the swf (which would simplifiy interaction a bit). You can do that by adding the classes to your include path an then create a new instance by doing
var mz:MegaZine = new MegaZine();